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; Map Reads with Appropriate Read Mapper
; Map Reads with Appropriate Read Mapper
: Currently, [bio-bwa.sourceforge.net/bwa.shtm BWA] is a convenient, widely used read mapper.
: Currently, [http://bio-bwa.sourceforge.net/bwa.shtm BWA] is a convenient, widely used read mapper.
; Mark Duplicate Reads
; Mark Duplicate Reads
; Recalibrate Base Quality Scores
; Recalibrate Base Quality Scores
: Base quality scores can be updated by comparing sites that are unlikely to vary (such as those not currently reported as variants in dbSNP or in the most recent [[1000 Genome Project]] analyses.
: Base quality scores can be updated by comparing sites that are unlikely to vary (such as those not currently reported as variants in dbSNP or in the most recent [http://www.1000genomes.org 1000 Genomes Project] analyses.
; Update Base Quality Score Metrics
; Update Base Quality Score Metrics
; Read Depth
; Read Depth
: Consider filtering out variants at sites where total read depth is unusually low. Unfortunately, capture protocols introduce very large amounts of variation in sequencing depth and it is usually not possible to accurately filter out sites sequenced at very high depth.
: Consider filtering out variants at sites where total read depth is unusually low. Unfortunately, capture protocols introduce very large amounts of variation in sequencing depth and it is usually not possible to accurately filter out sites sequenced at very high depth.
; Strand Bias
: Check whether each variant allele is supported by reads that map to both strands. Variants that are supported by reads on only one strand are almost always false positives.
= Special Considerations for Admixed Samples =
= Special Considerations for Admixed Samples =
